Nucleic acids and proteins from Group B Streptococcus

ABSTRACT

Protein antigens from Group B  Streptococcus  are described, together with nucleic acid sequences encoding them. Their use in vaccines and screening methods are described.

The present invention relates to proteins derived from Streptococcus agalactiae, nucleic acid molecules encoding such proteins, and the use of the proteins as antigens and/or immunogens and in detection/diagnosis. It also relates to a method for the rapid screening of bacterial genomes to isolate and characterise bacterial cell envelope associated or secreted proteins.

The Group B Streptococcus (GBS) (Streptococcus agalactiae) is an encapsulated bacterium which emerged in the 1970s as a major pathogen of humans causing sepsis and meningitis in neonates as well as adults. The incidence of early onset neonatal infection during the first 5 days of life varies from 0.7 to 3.7 per 1000 live births and causes mortality in about 20% of cases. Between 25-50% of neonates surviving early onset infections frequently suffer neurological sequalae. Late onset neonatal infections occur from 6 days to three months of age at a rate of about 0.5-1.0 per 1000 live births.

There is an established association between the colonisation of the maternal genetic tract by GBS at the time of birth and the risk of neonatal sepsis. In humans it has been established that the rectum may act as a reservoir for GBS. Susceptibility in the neonate is correlated with the a low concentration or absence of IgG antibodies to the capsular polysaccharides found on GBS causing human disease. In the USA strains isolated from clinical cases usually belong to capsular serotypes Ia, Ib, II, III although serotype V may be of increasing significance. Type VIII GBS is the major cause of neonatal sepsis in Japan.

A possible means of prevention involves intra or postpartum administration of antibiotics to the mother but there are concerns that this might lead to the emergence of resistant organisms and in some cases allergic reactions. Vaccination of the adolescent females to induce long lasting maternally derived immunity is one of the most promising approaches to prevent GBS infections in neonates. The capsular polysaccharide antigens of these organisms have attracted most attention as with regard to vaccine development. Studies in healthy adult volunteers have shown that serotype Ia, II and III polysaccharides are non-toxic and immunogenic in approximately 65%, 95% and 70% of non-immune adults respectively. One of the problems with using capsule antigens as vaccines is that the response rates vary according to pre-immunisation status and the polysaccharide antigen and not all vaccinees produce adequate levels of IgG antibody as indicated in vaccination studies with GBS polysaccharides in human volunteers.

Some people do not respond despite repeated stimuli. These properties are due to the T-independent nature of polysaccharide antigens. One strategy to enhance the immunogenicity of these vaccines is to enhance the T cell dependent properties of polysaccharides by conjugating them to a protein. The use of polysaccharide conjugates looks promising but there are still unresolved questions concerning the nature of the carrier protein. A conjugate vaccine against GBS would require at least 4 different conjugates to be prepared adding to the cost of a vaccine.

Recent evidence also suggests that bacterial surface proteins may be useful to confer immunity. A protein called Rib which is found on most serotype III strains but rarely on serotypes Ia, Ib or II confers immunity to challenge with Rib expressing GBS in animal models (Stalhammar-Carlemalm et al., Journal of Experimental Medicine 177:1593-1603 (1993)). Another surface protein of interest as a component of a vaccine is the alpha antigen of the C proteins which protected vaccinated mice against lethal infection with strains expressing alpha protein. The amount of antigen expressed by GBS strains varies markedly.

Approaches to vaccination against GBS infections which rely on the use of capsular polysaccharides have the disadvantage that response rates are likely to vary considerably according to pre-immunisation status and the particular type of polysaccharide antigen used. Results of trials in human volunteers have indicated that response rates may only be around 65% for some of the key capsule antigens (Larsson et al., Infection and Immunity 64:3518-3523 (1996)). It is also not clear whether all individuals responding to the vaccine would have adequate levels of polysaccharide specific IgG which can cross the placenta and afford immunity to neonates. By conjugating a protein carrier to the polysaccharide antigen it may be possible to convert them to T-cell dependent antigens and enhance their immunogenicity.

Preliminary studies with GBS type III polysaccharide-tetanus toxoid conjugate have been encouraging (Baker et al., Reviews of Infectious Diseases 7:458-467 (1985), Baker et al., The New England Journal of Medicine 319:1180-1185 (1988), Paoletti et al., Infection and Immunity 64:677-679 (1996), Paoletti et al., Infection and Immunity 62:3236-3243 (1994)) but in developed countries the use of tetanus may be disadvantageous since most adults will have been immunised against tetanus within the past five years. Additional boosters with tetanus toxoid may cause adverse reactions (Boyer., Current Opinions in Pediatrics 7:13-18 (1995)). The polysaccharide conjugate vaccines have the disadvantage of being costly to produce and manufacture in comparison with many other kinds of vaccines. There is also the possible risk of problems caused by the cross reactivity between GBS polysaccharides and sialic acid-containing human glycoproteins.

An alternative to polysaccharides as antigens is the use of protein antigens derived from GBS. Recent evidence suggest that the GBS surface associated proteins Rib and alpha C protein may be used to confer immunity to GBS infections in experimental model systems (Stalhammar-Carlemalm et al., (1993) [supra], Larsson et al., (1996) [supra]). However these two proteins are not conserved in all serotypes of GBS which cause disease in humans. Assuming that these antigens would be immunogenic and elicit protective level responses in humans they would not confer protection against all infections as 10% of infectious Group B streptococci do not express Rib or C protein alpha.

This invention seeks to overcome the problem of vaccination against GBS by using a novel screening method specifically designed to identify those Group B Streptococcus genes encoding bacterial cell surface associated or secreted proteins (antigens). The proteins expressed by these genes may be immunogenic, and therefore may be useful in the prevention and treatment of Group B Streptococcus infection. For the purposes of this application, the term immunogenic means that these proteins will elicit a protective immune response within a subject. Using this novel screening method a number of genes encoding novel Group B Streptococcus proteins have been identified.

Thus in a first aspect, the present invention provides a Group B Streptococcus protein, having a sequence selected from those shown in FIG. 1, or fragments or derivatives thereof.

It will be apparent to the skilled person that proteins and polypeptides included within this group may be cell surface receptors, adhesion molecules, transport proteins, membrane structural proteins, and/or signalling molecules.

Alterations in the amino acid sequence of a protein can occur which do not affect the function of a protein. These include amino acid deletions, insertions and substitutions and can result from alternative splicing and/or the presence of multiple translation start sites and stop sites. Polymorphisms may arise as a result of the infidelity of the translation process. Thus changes in amino acid sequence may be tolerated which do not affect the proteins function.

Thus, the present invention includes derivatives or variants of the proteins, polypeptides, and peptides of the present invention which show at least 50% identity to the proteins, polypeptides and peptides described herein. Preferably the degree of sequence identity is at least 60% and preferably it is above 75%. More preferably still is it above 80%, 90% or even 95%.

The term identity can be used to describe the similarity between two polypeptide sequences. A software package well known in the art for carrying out this procedure is the CLUSTAL program. It compares the amino acid sequences of two polypeptides and finds the optimal alignment by inserting spaces in either sequence as appropriate. The amino acid identity or similarity (identity plus conservation of amino acid type) for an optimal alignment can also be calculated using a software package such as BLASTx. This program aligns the largest stretch of similar sequence and assigns a value to the fit. For any one pattern comparison several regions of similarity may be found, each having a different score. One skilled in the art will appreciate that two polypeptides of different lengths may be compared over the entire length of the longer fragment. Alternatively small regions may be compared. Normally sequences of the same length are compared for a useful comparison to be made.

Manipulation of the DNA encoding the protein is a particularly powerful technique for both modifying proteins and for generating large quantities of protein for purification purposes. This may involve the use of PCR techniques to amplify a desired nucleic acid sequence. Thus the sequence data provided herein can be used to design primers for use in PCR so that a desired sequence can be targeted and then amplified to a high degree.

Typically primers will be at least five nucleotides long and will generally be at least ten nucleotides long (e.g. fifteen to twenty-five nucleotides long). In some cases primers of at least thirty or at least thirty-five nucleotides in length may be used.

As a further alternative chemical synthesis may be used. This may be automated. Relatively short sequences may be chemically synthesised and ligated together to provide a longer sequence.

Thus in a further aspect, the present invention provides, a nucleic acid molecule comprising or consisting of a sequence which is:

-   -   (i) any of the DNA sequences set out in FIG. 1 herein or their         RNA equivalents;     -   (ii) a sequence which is complementary to any of the sequences         of (i);     -   (iii) a sequence which codes for the same protein or         polypeptide, as those sequences of (i) or (ii);     -   (iv) a sequence which is shows substantial identity with any of         those of (i), (ii) and (iii); or     -   (v) a sequence which codes for a derivative or fragment of a         nucleic acid molecule shown in FIG. 1.

The term identity can also be used to describe the similarity between two individual DNA sequences. The ‘bestfit’ program (Smith and Waterman, Advances in applied Mathematics, 482-489 (1981)) is one example of a type of computer software used to find the best segment of similarity between two nucleic acid sequences, whilst the GAP program enables sequences to be aligned along their whole length and finds the optimal alignment by inserting spaces in either sequence as appropriate.

The term ‘RNA equivalent’ when used above indicates that a given RNA molecule has a sequence which is complementary to that of a given DNA molecule, allowing for the fact that in RNA ‘U’ replaces ‘T’ in the genetic code. The nucleic acid molecule may be in isolated or recombinant form.

The nucleic acid molecule may be in an isolated or recombinant form. DNA constructs can readily be generated using methods well known in the art. These techniques are disclosed, for example in J. Sambrook et al, Molecular Cloning 2^(nd) Edition; Cold Spring Harbour Laboratory Press (1989). Modifications of DNA constructs and the proteins expressed such as the addition of promoters, enhancers, signal sequences, leader sequences, translation start and stop signals and DNA stability controlling regions, or the addition of fusion partners may then be facilitated.

Normally the DNA construct will be inserted into a vector which may be of phage or plasmid origin. Expression of the protein is achieved by the transformation or transfection of the vector into a host cell which may be of eukaryotic or prokaryotic origin. Such vectors and suitable host cells form yet further aspects of the present invention.

The Group B Streptococcus proteins (antigens) described herein can additionally be used to raise antibodies, or to generate affibodies. These can be used to detect Group B Streptococcus.

Thus in a further aspect the present invention provides, an antibody, affibody, or a derivative thereof which binds to any one or more of the proteins, polypeptides, peptides, fragments or derivatives thereof, as described herein.

Antibodies within the scope of the present invention may be monoclonal or polyclonal. Polyclonal antibodies can be raised by stimulating their production in a suitable animal host (e.g. a mouse, rat, guinea pig, rabbit, sheep, goat or monkey) when a protein as described herein, or a homologue, derivative or fragment thereof, is injected into the animal. If desired, an adjuvant may be administered together with the protein. Well-known adjuvants include Freund's adjuvant (complete and incomplete) and aluminium hydroxide. The antibodies can then be purified by virtue of their binding to a protein as described herein.

Monoclonal antibodies can be produced from hybridomas. These can be formed by fusing myeloma cells and spleen cells which produce the desired antibody in order to form an immortal cell line. Thus the well-known Kohler & Milstein technique (Nature 256 (1975)) or subsequent variations upon this technique can be used.

Techniques for producing monoclonal and polyclonal antibodies that bind to a particular polypeptide/protein are now well developed in the art. They are discussed in standard immunology textbooks, for example in Roitt et al, Immunology second edition (1989), Churchill Livingstone, London.

In addition to whole antibodies, the present invention includes derivatives thereof which are capable of binding to proteins etc as described herein. Thus the present invention includes antibody fragments and synthetic constructs. Examples of antibody fragments and synthetic constructs are given by Dougall et al in Tibtech 12 372-379 (September 1994).

Antibody fragments include, for example, Fab, F(ab′)₂ and Fv fragments. Fab fragments (These are discussed in Roitt et al [supra]). Fv fragments can be modified to produce a synthetic construct known as a single chain Fv (scFv) molecule. This includes a peptide linker covalently joining V_(h) and V_(l) regions, which contributes to the stability of the molecule. Other synthetic constructs that can be used include CDR peptides. These are synthetic peptides comprising antigen-binding determinants. Peptide mimetics may also be used. These molecules are usually conformationally restricted organic rings that mimic the structure of a CDR loop and that include antigen-interactive side chains.

Synthetic constructs include chimaeric molecules. Thus, for example, humanised (or primatised) antibodies or derivatives thereof are within the scope of the present invention. An example of a humanised antibody is an antibody having human framework regions, but rodent hypervariable regions. Ways of producing chimaeric antibodies are discussed for example by Morrison et al in PNAS, 81, 6851-6855 (1984) and by Takeda et al in Nature. 314, 452-454 (1985).

Synthetic constructs also include molecules comprising an additional moiety that provides the molecule with some desirable property in addition to antigen binding. For example the moiety may be a label (e.g. a fluorescent or radioactive label). Alternatively, it may be a pharmaceutically active agent.

Affibodies are proteins which are found to bind to target proteins with a low dissociation constant. They are selected from phage display libraries expressing a segment of the target protein of interest (Nord K, Gunneriusson E, Ringdahl J, Stahl S, Uhlen M, Nygren P A, Department of Biochemistry and Biotechology, Royal Institute of Technology (KTH), Stockholm, Sweden).

In a further aspect the invention provides an immunogenic composition comprising one or more proteins, polypeptides, peptides, fragments or derivatives thereof, or nucleotide sequences described herein. A composition of this sort may be useful in the treatment or prevention of Group B Streptococcus infection in subject. In a preferred aspect of the invention the immunogenic composition is a vaccine.

In other aspects the invention provides:

-   i) Use of an immunogenic composition as described herein in the     preparation of a medicament for the treatment or prophylaxis of     Group B Streptococcus infection. Preferably the medicament is a     vaccine. -   ii) A method of detection of Group B Streptococcus which comprises     the step of bringing into contact a sample to be tested with at     least one antibody, affibody, or a derivative thereof, as described     herein. -   iii) A method of detection of Group B Streptococcus which comprises     the step of bringing into contact a sample to be tested with at     least one protein, polypeptide, peptide, fragments or derivatives as     described herein. -   iv) A method of detection of Group B Streptococcus which comprises     the step of bringing into contact a sample to be tested with at     least one nucleic acid molecule as described herein. -   v) A kit for the detection of Group B Streptococcus comprising at     least one antibody, affibody, or derivatives thereof, described     herein. -   vi). A kit for the detection of Group B Streptococcus comprising at     least one Group B Streptococcus protein, polypeptide, peptide,     fragment or derivative thereof, as described herein. -   vii) A kit for the detection of Group B Streptococcus comprising at     least one nucleic acid of the invention.

As described previously, the novel proteins described herein are identified and isolated using a novel screening method which specifically identifies those Group B Streptococcus genes encoding bacterial cell envelope associated or secreted proteins.

The information necessary for the secretion/export of proteins has been extensively studied in bacteria. In the majority of cases, export requires a signal peptide positioned at the N-terminus of the precursor protein to target the precursor to translocation sites on the membrane. During or after translocation, the signal peptide is removed by a signal peptidase. The ultimate destination/localisation of the protein, (whether it be secreted extracellularly or anchored to the bacterium's surface, etc) is determined by sequences other than the leader peptide sequence.

Recently, Poquet et al. (J. Bacteriol. 180:1904-1912 (1998)) have described a screening vector incorporating the nuc gene lacking its own signal leader as a reporter to identify exported proteins in Gram positive bacteria, and have applied it to L. lactis. Staphylococcal nuclease is a naturally secreted heat-stable, monomeric enzyme which has been efficiently expressed and secreted in a range of Gram positive bacteria (Shortle., Gene 22:181-189 (1983), Kovacevic et al., J. Bacteriol. 162:521-528 (1985), Miller et al., J. Bacteriol. 169:3508-3514 (1987), Liebl et al., J. Bacteriol. 174:1854-1861(1992), Le Loir et al., J. Bacteriol. 176:5135-5139 (1994), Poquet et al., 1998 [supra]). The screening vector (pFUN) contains the pAMβ1 replicon which functions in a broad host range of Gram-positive bacteria in addition to the ColE1 replicon that promotes replication in Escherichia coli and certain other Gram negative bacteria. Unique cloning sites present in the vector can be used to generate transcriptional and translational fusions between cloned genomic DNA fragments and the open reading frame of the truncated nuc gene devoid of its own signal secretion leader. The nuc gene makes an ideal reporter gene because the secretion of nuclease can readily be detected using a simple and sensitive plate test: Recombinant colonies secreting the nuclease develop a pink halo whereas control colonies remain white (Shortle, 1983 [supra], Le Loir et al., 1994 [supra]).

A direct screen to identify and isolate DNA encoding bacterial cell envelope associated or secreted proteins (antigens) in pathogenic bacteria has been developed by the present inventors which utilises a vector-system (pTREP1 expression vector) in Lactococcus lactis that specifically detects DNA sequences which are adjacent to, and associated with DNA encoding surface proteins from Group B Streptococcus. The screening vector also incorporates the nuc gene encoding the Staphylococcal nuclease as a reporter gene.

Only the part of the nuc gene encoding the mature nuclease protein (minus its signal peptide sequence) is cloned into the pTREP1 expression vector in L. lactis. In this form, the nuc-encoded nuclease cannot be secreted even when expressed intracellularly. The reporter vector is then randomly combined with appropriately digested genomic DNA from Group B Streptococcus, cloned into L. lactis and used as a screening system for sequences permitting the export of nuclease. In this way gene/partial gene sequences encoding exported proteins from Group B Streptococcus are isolated. Once a partial gene sequence is obtained, full length sequences encoding exported proteins can readily be obtained using techniques well known in the art.

In possessing a promoter, the pTREP1-nuc vectors differ from the pFUN-vector described by Poquet et al. (1998) [supra], which was used to identify L. lactis exported proteins by screening directly for Nuc activity directly in L. lactis. As the pFUN vector does not contain a promoter upstream of the nuc open reading frame the cloned genomic DNA fragment must also provide the signals for transcription in addition to those elements required for translation initiation and secretion of Nuc. This limitation may prevent the isolation of genes that are distant from a promoter for example genes which are within polycistronic operons. Additionally there can be no guarantee that promoters derived from other species of bacteria will be recognised and functional in L. lactis. Certain promoters may be under stringent regulation in the natural host but not in L. lactis. In contrast, the presence of the P1 promoter in the pTREP1-nuc series of vectors ensures that promoterless DNA fragments (or DNA fragments containing promoter sequences not active in L. lactis) may still be transcribed. Thus yet another advantage of this invention is that genes missed in other screening methods may be identified.

Hence in a further aspect the present invention provides a method of screening for DNA encoding bacterial cell wall associated or surface antigens in gram positive bacteria comprising the steps of:

-   -   combining a reporter vector including the nucleotide sequence         encoding the mature from of the staphylcoccus nuclease gene and         an upstream promoter region with DNA from a gram positive         bacteria.     -   transforming the resultant vector into Lactococcus lactis cells.     -   assaying for the secretion of staphlycoccus nuclease protein in         the transformed cells.

Preferably, the reporter vector is one of the pTREP1-nuc vectors shown in FIG. 4.

In another aspect, the present invention provides a vector as shown in FIG. 4 for use in screening for DNA encoding exported or surface antigens in gram positive bacteria. Examples of gram positive bacteria which may be screened include Group B Streptococcus, Streptococcus pneumoniae, Staphylcoccus aureus or pathogenic Group A Streptococci.

Given that the inventors have identified a group of important proteins, such proteins are potential targets for anti-microbial therapy. It is necessary, however, to determine whether each individual protein is essential for the organism's viability. Thus, the present invention also provides a method of determining whether a protein or polypeptide as described herein represents a potential anti-microbial target which comprises inactivating said protein and determining whether Group B Streptococcus is still viable.

A suitable method for inactivating the protein is to effect selected gene knockouts, ie prevent expression of the protein and determine whether this results in a lethal change. Suitable methods for carrying out such gene knockouts are described in Li et al, P.N.A.S., 94:13251-13256 (1997) and Kolkman et al

In a final aspect the present invention provides the use of an agent capable of antagonising, inhibiting or otherwise interfering with the function or expression of a protein or polypeptide of the invention in the manufacture of a medicament for use in the treatment or prophylaxis of Group B Streptococcus infection.

The invention will now be described by means of the following example which should not in any way be construed as limiting. The examples refer to the figures in which

FIG. 1: (A) Shows a number of full length nucleotide sequences encoding antigenic Group B Streptococcus proteins. (B) Shows the corresponding amino acid sequences.

FIG. 2: Shows a number of oligonucleotide primers used in the screening process

-   -   nucS1 primer designed to amplify a mature form of the nuc A gene     -   nucS2—primer designed to amplify a mature form of the nuc A         gene.     -   nucS3 primer designed to amplify a mature form of the nuc A gene     -   nucR primer designed to amplify a mature form of the nuc A gene     -   nucseq primer designed to sequence DNA cloned into the pTREP-Nuc         vector     -   pTREP_(F) nucleic acid sequence containing recognition site for         ECORV. Used for cloning fragments into pTREX7.     -   pTREP_(R) nucleic acid sequence containing recognition site for         BAMH1. Used for cloning fragments into pTREX7.     -   PUC_(F) forward sequencing primer, enables direct sequencing of         cloned DNA fragments.     -   V_(R) example of gene specific primer used to obtain further         antigen DNA sequence by the method of DNA walking.     -   V₁ example of gene specific primer used to obtain further         antigen DNA sequence by the method of DNA walking.     -   V₂ example of gene specific primer used to obtain further         antigen DNA sequence by the method of DNA walking.

FIG. 3: (i) Schematic presentation of the nucleotide sequence of the unique gene cloning site immediately upstream of the mature nuc gene in pTREP1-nuc1, pTREP1-nuc2 and pTREP1-nuc3. Each of the pTREP-nuc vectors contain an EcoRV (a SmaI site in pTREP1-nuc2) cleavage site which allows cloning of genomic DNA fragments in 3 different frames with respect to the mature nuc gene.

-   -   (ii) A physical and genetic summary map of the pTREP1-nuc         vectors. The expression cassette incorporating nuc, the         macrolides, lincosamides and streptogramin B (MLS) resistance         determinant, and the replicon (rep) Ori-pAMβ1 are depicted (not         drawn to scale).     -   (iii) Schematic presentation of the expression cassette showing         the various sequence elements involved in gene expression and         location of unique restriction endonuclease sites (not drawn to         scale).

FIG. 4: Shows the results of various DNA vaccine trials;

FIG. 5: Shows the results of a second group of DNA vaccine trials;

FIGS. 6-11: Show various Southern Blot analyses of different Group B streptococcus strains.

EXAMPLE 1

Thus far more than 100 gene/partial gene sequences putatively encoding exported proteins in S. agalactiae have been identified using the nuclease screening system of the invention. These have been further analysed to remove artifacts. The nucleotide sequences of genes identified using the screening system has been characterised using a number of parameters described below. All of these sequences are novel in that they have not been described previously.

1. All putative surface proteins are analysed for leader/signal peptide sequences. Bacterial signal peptide sequences share a common design. They are characterised by a short positively charged N-terminus (N region) immediately preceding a stretch of hydrophobic residues (central portion-h region) followed by a more polar C-terminal portion which contains the cleavage site (c-region). Computer software is used to perform hydropathy profiling of putative proteins (Marcks, Nuc. Acid. Res., 16:1829-1836 (1988)) which is used to identify the distinctive hydrophobic portion (h-region) typical of leader peptide sequences. In addition, the presence/absence of a potential ribosomal binding site (Shine-Dalgarno sequence required for translation) is also noted.

2. All putative surface protein sequences are used to search the OWL sequence database which includes a translation of the GENBANK and SWISSPROT database. This allows identification of similar sequences which may have been previously characterised not only at the sequence level but at a functional level. It may also provide information indicating that these proteins are indeed surface related and not artifacts.

3. Putative S. agalactiae surface proteins are also be assessed for their novelty. Some of the identified proteins may or may not possess a typical leader peptide sequence and may not show homology with any DNA/protein sequences in the database. Indeed these proteins may indicate the primary advantage of our screening method, i.e. isolating atypical surface-related proteins, which would have been missed in all previously described screening protocols.

The construction of three reporter vectors and their use in L. lactis to identify and isolate genomic DNA fragments from pathogenic bacteria encoding secreted or surface associated proteins is now described.

Construction of the pTREP1-nuc Series of Reporter Vectors

(a) Construction of Expression Plasmid pTREP1

The pTREP1 plasmid is a high-copy number (40-80 per cell) theta-replicating gram positive plasmid, which is a derivative of the pTREX plasmid which is itself a derivative of the the previously published pIL253 plasmid. pIL253 incorporates the broad Gram-positive host range replicon of pAMβ1 (Simon and Chopin, 1988) and is non-mobilisable by the L lactis sex-factor. pIL253 also lacks the tra function which is necessary for transfer or efficient mobilisation by conjugative parent plasmids exemplified by pIL501. The Enterococcal pAMβ1 replicon has previously been transferred to various species including Streptococcus, Lactobacillus and Bacillus species as well as Clostridium acetobutylicum, (LeBlanc et al., Proceedings of the National Academy of Science USA 75:3484-3487 (1978)) indicating the potential broad host range utility. The pTREP1 plasmid represents a constitutive transcription vector.

The pTREX vector was constructed as follows. An artificial DNA fragment containing a putative RNA stabilising sequence, a translation initiation region (TIR), a multiple cloning site for insertion of the target genes and a transcription terminator was created by annealing 2 complementary oligonucleotides and extending with Tfl DNA polymerase. The sense and anti-sense oligonucleotides contained the recognition sites for NheI and BamHI at their 5′ ends respectively to facilitate cloning. This fragment was cloned between the XbaI and BamHI sites in pUC19NT7, a derivative of pUC19 which contains the T7 expression cassette from pLET1 (Wells et al., J. Appl. Bacteriol. 74:629-636 (1993)) cloned between the EcoRI and HindIII sites. The resulting construct was designated pUCLEX. The complete expression cassette of pUCLEX was then removed by cutting with HindIII and blunting followed by cutting with EcoRI before cloning into EcoRI and SacI (blunted) sites of pIL253 to generate the vector pTREX (Wells and Schofield, In Current advances in metabolism, genetics and applications-NATO ASI Series. H 98:37-62. (1996)). The putative RNA stabilising sequence and TIR are derived from the Escherichia coli T7 bacteriophage sequence and modified at one nucleotide position to enhance the complementarity of the Shine Dalgamo (SD) motif to the ribosomal 16s RNA of Lactococcus lactis (Schofield et al. pers. coms. University of Cambridge Dept. Pathology.).

A Lactococcus lactis MG1363 chromosomal DNA fragment exhibiting promoter activity which was subsequently designated P7 was cloned between the EcoRI and BglII sites present in the expression cassette, creating pTREX7. This active promoter region had been previously isolated using the promoter probe vector pSB292 (Waterfield et al., Gene 165:9-15 (1995)). The promoter fragment was amplified by PCR using the Vent DNA polymerase according to the manufacturer.

The pTREP1 vector was then constructed as follows. An artificial DNA fragment which included a transcription terminator, the forward pUC sequencing primer, a promoter multiple cloning site region and a universal translation stop sequence was created by annealing two overlapping partially complementary synthetic oligonucleotides together and extending with sequenase according to manufacturers instructions. The sense and anti-sense (pTREP_(F) and pTREP_(R)) oligonucleotides contained the recognition sites for EcoRV and BamHI at their 5′ ends respectively to facilitate cloning into pTREX7. The transcription terminator was that of the Bacillus penicillinase gene, which has been shown to be effective in Lactococcus (Jos et al., Applied and Environmental Microbiology 50:540-542 (1985)). This was considered necessary as expression of target genes in the pTREX vectors was observed to be leaky and is thought to be the result of cryptic promoter activity in the origin region (Schofield et al. pers. coms. University of Cambridge Dept. Pathology.). The forward pUC primer sequencing was included to enable direct sequencing of cloned DNA fragments. The translation stop sequence which encodes a stop codon in 3 different frames was included to prevent translational fusions between vector genes and cloned DNA fragments. The pTREX7 vector was first digested with EcoRI and blunted using the 5′-3′ polymerase activity of T4 DNA polymerase (NEB) according to manufacturer's instructions. The EcoRI digested and blunt ended pTREX7 vector was then digested with Bgl II thus removing the P7 promoter. The artificial DNA fragment derived from the annealed synthetic oligonucleotides was then digested with EcoRV and Bam HI and cloned into the EcoRI(blunted)-Bgl II digested pTREX7 vector to generate pTREP. A Lactococcus lactis MG1363 chromosomal promoter designated P1 was then cloned between the EcoRI and BglII sites present in the pTREP expression cassette forming pTREP1. This promoter was also isolated using the promoter probe vector pSB292 and characterised by Waterfield et al., (1995) [supra]. The P1 promoter fragment was originally amplified by PCR using vent DNA polymerase according to manufacturers instructions and cloned into the pTREX as an EcoRI-BglII DNA fragment. The EcoRI-BglII P1 promoter containing fragment was removed from pTREX1 by restriction enzyme digestion and used for cloning into pTREP (Schofield et al. pers. coms. University of Cambridge, Dept. Pathology.).

(b) PCR Amplification of the S. aureus nuc Gene.

The nucleotide sequence of the S. aureus nuc gene (EMBL database accession number V01281) was used to design synthetic oligonucleotide primers for PCR amplification. The primers were designed to amplify the mature form of the nuc gene designated nucA which is generated by proteolytic cleavage of the N-terminal 19 to 21 amino acids of the secreted propeptide designated Snase B (Shortle, 1983 [supra]). Three sense primers (nucS1, nucS2 and nucS3, shown in FIG. 3) were designed, each one having a blunt-ended restriction endonuclease cleavage site for EcoRV or SmaI in a different reading frame with respect to the nuc gene. Additionally BglII and BamHI were incorporated at the 5′ ends of the sense and anti-sense primers respectively to facilitate cloning into BamHI and BglII cut pTREP1. The sequences of all the primers are given in FIG. 3. Three nuc gene DNA fragments encoding the mature form of the nuclease gene (NucA) were amplified by PCR using each of the sense primers combined with the anti-sense primer. The nuc gene fragments were amplified by PCR using S. aureus genomic DNA template, Vent DNA Polymerase (NEB) and the conditions recommended by the manufacturer. An initial denaturation step at 93° C. for 2 min was followed by 30 cycles of denaturation at 93° C. for 45 sec, annealing at 50° C. for 45 seconds, and extension 73° C. for 1 minute and then a final 5 min extension step at 73° C. The PCR amplified products were purified using a Wizard clean up column (Promega) to remove unincorporated nucleotides and primers.

(c) Construction of the pTREP1-nuc Vectors

The purified nuc gene fragments described in section b were digested with Bgl II and BamHI using standard conditions and ligated to BamHI and BglII cut and dephosphorylated pTREP1 to generate the pTREP1-nuc1, pTREP1-nuc2 and pTREP1-nuc3 series of reporter vectors. These vectors are described in FIG. 4. General molecular biology techniques were carried out using the reagents and buffers supplied by the manufacturer or using standard techniques (Sambrook and Maniatis, Molecular cloning: A laboratory manual. Cold Spring Harbor Laboratory Press: Cold Spring Harbour (1989)). In each of the pTREP1-nuc vectors the expression cassette comprises a transcription terminator, lactococcal promoter P1, unique cloning sites (BglII, EcoRV or SmaI) followed by the mature form of the nuc gene and a second transcription terminator. Note that the sequences required for translation and secretion of the nuc gene were deliberately excluded in this construction. Such elements can only be provided by appropriately digested foreign DNA fragments (representing the target bacterium) which can be cloned into the unique restriction sites present immediately upstream of the nuc gene.

(d) Screening for Secreted Proteins in Group B Streptococcus.

Genomic DNA isolated from and Group B Streptococcus (S. agalactiae) was digested with the restriction enzyme Tru9I. This enzyme which recognises the sequence 5′-TTAA-3′ was used because it cuts A/T rich genomes efficiently and can generate random genomic DNA fragments within the preferred size range (usually averaging 0.5-1.0 kb). This size range was preferred because there is an increased probability that the P1 promoter can be utilised to transcribe a novel gene sequence. However, the P1 promoter may not be necessary in all cases as it is possible that many Streptococcal promoters are recognised in L. lactis. DNA fragments of different size ranges were purified from partial Tru9I digests of and S. agalactiae genomic DNA. As the Tru 9I restriction enzyme generates staggered ends the DNA fragments had to be made blunt ended before ligation to the EcoRV or SmaI cut pTREP1-nuc vectors. This was achieved by the partial fill-in enzyme reaction using the 5′-3′ polymerase activity of Klenow enzyme. Briefly Tru9I digested DNA was dissolved in a solution (usually between 10-20 μl in total) supplemented with T4 DNA ligase buffer (New England Biolabs; NEB) (1×) and 33 μM of each of the required dNTPs, in this case dATP and dTTP. Klenow enzyme was added (1 unit Klenow enzyme (NEB) per μg of DNA) and the reaction incubated at 25° C. for 15 minutes. The reaction was stoped by incubating the mix at 75° C. for 20 minutes. EcoRV or SmaI digested pTREP-nuc plasmid DNA was then added (usually between 200-400 ng). The mix was then supplemented with 400 units of T4 DNA ligase (NEB) and T4 DNA ligase buffer (1×) and incubated overnight at 16° C. The ligation mix was precipiated directly in 100% Ethanol and 1/10 volume of 3M sodium acetate (pH 5.2) and used to transform L. lactis MG1363 (Gasson, J. Bacteriol. 154:1-9 (1983)). Alternatively, the gene cloning site of the pTREP-nuc vectors also contains a BglII site which can be used to clone for example Sau3AI digested genomic DNA fragments.

L. lactis transformant colonies were grown on brain heart infusion agar and nuclease secreting (Nuc⁺) clones were detected by a toluidine blue-DNA-agar overlay (0.05 M Tris pH 9.0, 10 g of agar per litre, 10 g of NaCl per liter, 0.1 mM CaCl2, 0.03% wt/vol. salmon sperm DNA and 90 mg of Toluidine blue O dye) essentially as described by Shortle, 1983 [supra], and Le Loir et al., 1994 [supra]). The plates were then incubated at 37° C. for up to 2 hours. Nuclease secreting clones develop an easily identifiable pink halo. Plasmid DNA was isolated from Nuc⁺ recombinant L. lactis clones and DNA inserts were sequenced on one strand using the NucSeq sequencing primer described in FIG. 3, which sequences directly through the DNA insert.

Whilst the example described above related specifically to Group B Streptococcus, it will be apparent to one skilled in the art that the same screening technique may be used to detect exported and secreted proteins in other gram positive bacteria, for example Streptococcus pneumoniae.

EXAMPLE 2 Screening Group B Streptococcal Derived Genes in DNA Vaccination Experiments

pcDNA3.1+ as a DNA Vaccine Vector

The commercially available pcDNA3.1+ plasmid (Invitrogen), referred to as pcDNA3.1 henceforth, was used as a vector in all DNA immunisation experiments involving gene targets derived using the LEEP system. pcDNA 3.1 is designed for high-level stable and transient expression in mammalian cells and has been used widely and successfully as a host vector to test candidate genes from a variety of pathogens in DNA vaccination experiments (Zhang et al., 1997; Kurar and Splitter, 1997; Anderson et al., 1996).

The vector possesses a multiple cloning site which facilitates the cloning of multiple gene targets downstream of the human cytomegalovirus (CMV) immediate-early promoter/enhancer which permits efficient, high-level expression of the target gene in a wide variety of mammalian cells and cell types including both muscle and immune cells. This is important for optimal immune response as it remains unknown as to which cells types are most important in generating a protective response in vivo. The plasmid also contains the ColE1 origin of replication which allows convenient high-copy number replication and growth in E. coli and the ampicillin resistance gene (B-lactamase) for selection in E. coli. In addition pcDNA 3.1 possesses a T7 promoter/priming site upstream of the MCS which allows for in vitro transcription of a cloned gene in the sense orientation.

Preparation of DNA Vaccines

Oligonucleotide primers were designed for each individual gene of interest derived using the LEEP system. Each gene was examined thoroughly, and where possible, primers were designed such that they targeted that portion of the gene thought to encode only the mature portion of the protein (APPENDIX I). It was hoped that expressing those sequences that encode only the mature portion of a target gene protein, would facilitate its correct folding when expressed in mammalian cells. For example, in the majority of cases primers were designed such that putative N-terminal signal peptide sequences would not be included in the final amplification product to be cloned into the pcDNA3.1 expression vector. The signal peptide directs the polypeptide precursor to the cell membrane via the protein export pathway where it is normally cleaved off by signal peptidase I (or signal peptidase II if a lipoprotein). Hence the signal peptide does not make up any part of the mature protein whether it be displayed on the bacterium's surface or secreted. Where a N-terminal leader peptide sequence was not immediately obvious, primers were designed to target the whole of the gene sequence for cloning and ultimately, expression in pcDNA3.1.

All forward and reverse oligonucleotide primers incorporated appropriate restriction enzyme sites to facilitate cloning into the pcDNA3.1 MCS region. All forward primers were also designed to include the conserved Kozak nucleotide sequence 5′-gccacc-3′ immediately upstream of an ‘atg’ translation initiation codon in frame with the target gene insert. The Kozak sequence facilitates the recognition of initiator sequences by eukaryotic ribosomes. Typically, a forward primer incorporating a BamH1 restriction enzyme site the primer would begin with the sequence 5′-cgggatccgccaccatg-3′, followed by a sequence homologous to the 5′ end of that part of a gene being amplified. All reverse primers incorporated a Not I restriction enzyme site sequence 5′-ttgcggccgc-3′. All gene-specific forward and reverse primers were designed with compatible melting temperatures to facilitate their amplification.

All gene targets were amplified by PCR from S. agalactiae genomic DNA template using Vent DNA polymerase (NEB) or rTth DNA polymerase (PE Applied Biosystems) using conditions recommended by the manufacturer. A typical amplification reaction involved an initial denaturation step at 95° C. for 2 minutes followed by 35 cycles of denaturation at 95° C. for 30 seconds, annealing at the appropriate melting temperature for 30 seconds, and extension at 72° C. for 1 minute (1 minute per kilobase of DNA being amplified). This was followed by a final extension period at 72° C. for 10 minutes. All PCR amplified products were extracted once with phenol chloroform (2:1:1) and once with chloroform (1:1) and ethanol precipitated.

Specific DNA fragments were isolated from agarose gels using the QIAquick Gel Extraction Kit (Qiagen). The purified amplification gene DNA fragments were digested with the appropriate restriction enzymes and cloned into the pcDNA3.1 plasmid vector using E. coli as a host. Successful cloning and maintenance of genes was confirmed by restriction mapping and by DNA sequencing. Recombinant plasmid DNA was isolated on a large scale (>1.5 mg) using Plasmid Mega Kits (Qiagen).

It was decided to include the S. agalactiae rib gene as a positive control in at least one trial of DNA immunisation experiments. Rabbit antiserum against the Rib protein (Stalhammar-Carleman et al., 1993) and highly purified preparations of the Rib protein itself (Larsson et al., 1999; Larsson et al., 1996) have been shown to confer protection against lethal infection with strains expressing the antigen. All serotype III strains have been shown to express the Rib antigen and Southern blot analysis performed in the laboratory has confirmed that S. agalactiae serotype III (strain 97/0099) does contain the rib gene, hence the rib gene as part of a DNA vaccine would represent a potential positive control for all DNA immunisation experiments. Oligonucleotide primers were designed (Appendix I) that targeted only the mature portion of the rib gene and which included appropriate restriction enzyme sites for cloning into pcDNA3.1. rib was amplified using rTth DNA polymerase (PE Applied Biosystems) using conditions recommended by the manufacturer. Conditions for cloning were similar to that described previously.

Preparation of a S. agalactiae Standard Inoculum

Strain Validation

S. agalactiae serotype III (strain 97/0099) is a recent clinical isolate derived from the cerebral spinal fluid of a new born baby suffering from meningitis. This haemolytic strain of Group B Streptococcus was epidemiologically tested and validated at the Respiratory and Systemic Infection Laboratory, PHLS Central Public health laboratory, 61 Collindale Avenue, London NW9 5HT. The strain was subcultured only twice prior to its arrival in the laboratory. Upon its arrival on a agar slope, a sweep of 4-5 colonies was immediately used to inoculate a Todd Hewitt/5% horse blood broth which was incubated overnight statically at 37 C. 0.5 ml aliquots of this overnight culture were then used to make 20% glycerol stocks of the bacterium for long term storage at −70 C. Glyerol stocks were streaked on Todd Hewitt/5% horse blood agar plates to confirm viability.

In Vivo Passaging of Group B Streptoccocus

A frozen culture (described under strain validation) of S. agalactiae serotype III (strain 97/0099) was streaked to single colonies on Todd-Hewitt/5% blood agar plates which were incubated overnight at 37° C. A sweep of 4-5 colonies was used to inoculate a Todd Hewitt/5% horse blood broth which was again incubated overnight. A 0.5 ml aliquot from this overnight culture was used to inoculate a 50 ml Todd Hewitt broth (1:100 dilution) which was incubated at 37 C. 10-fold serial dilutions of the overnight culture were made (since virulence of this strain was unknown) and each were passaged intra-peritoneally (IP) in CBA/ca mice in duplicate. Viable counts were performed on the various inocula used in the passage. Groups of mice were challenged with various concentrations of the pathogen ranging from 10⁸ to 10⁴ colony forming units (cfu). Mice that developed symptoms were terminally anaesthetized and cardiac punctures were performed (Only mice that had been challenged with the highest doses, i.e. 1×10⁸ cfu, developed symptoms). The retrieved unclotted blood was used to inoculate directly a 50 ml serum broth (Todd Hewitt/20% inactivated foetal calf serum). The culture was constantly monitored and allowed to grow to late logarithmic phase. The presence of blood in the medium interfered with OD₆₀₀ readings as it was being increasingly lysed with increasing growth of the bacterium, hence the requirement to constantly monitor the culture. Upon reaching late logarithmic phase/early stationary phase, the culture was transferred to a fresh 50 ml tube in order to exclude dead bacterial cells and remaining blood cells which would have sedimented at the bottom of the tube. 0.5 ml aliquots were then transferred to sterile cryovials, frozen in liquid nitrogen and stored at −70 C. A viable count was carried out on a single standard inoculum aliquot in order to determine bacterial numbers. This was determined to be approximately 5×10⁸ cfu per ml.

Intra-Peritoneal Challenge and Virulence Testing of Group B Streptococcus Standard Inoculum

To determine if the standard inoculum was suitably virulent for use in a vaccine trial, challenges were carried out using a dose range. Frozen standard inoculum strain aliquots were allowed to thaw at room temperature. From viable count data the number of cfu per ml was already known for the standard inoculum. Initially, serial dilutions of the standard inoculum were made in Todd Hewitt broth and mice were challenged intra-peritoneally with doses ranging from 1×10⁸ to 1×10⁴ cfu in a 500 μl volume of Todd Hewitt broth. The survival times of mouse groups injected with different doses of the bacterium were compared. The standard inoculum was determined to be suitably virulent and a dose of 1×10⁶ cfu was considered close to optimal for further use in vaccine trials. Further optimisation was carried out by comparing mice challenged with doses ranging between 5×10⁵ and 5×10⁶ cfu. The optimal dose was estimated to be approximately 2.5×10⁶ cfu. This represented a 100% lethal dose and was repeatedly consistant with end-points as determined by survival times being clustered within a narrow time-range. Throughout all these experiments, challenged mice were constantly monitored to clarify symptoms, stages of symptom development as well as calculating survival times.

Vaccine Trials

Vaccine trials in mice were accomplished by the administration of DNA to 6 week old CBA/ca mice (Harlan, UK). Mice to be vaccinated were divided into groups of six and each group were immunised with recombinant pcDNA3.1 plasmid DNA containing a specific target-gene sequence derived using the LEEP system. A total of 100 μg of DNA in Dulbecco's PBS (Sigma) was injected intramuscularly into the tibialis anterior muscle of both hind legs. Four weeks later this procedure was repeated using the same amount of DNA. For comparison, control mice groups were included in all vaccine trials. These control groups were either not DNA-vaccinated or were immunised with non-recombinant pcDNA3.1 plasmid DNA only, using the same time course described above. Four weeks after the second immunisation, all mice groups were challenged intra-peritoneally with a lethal dose of S. agalactiae serotype III (strain 97/0099). The actual number of bacteria administered was determined by plating serial dilutions of the inoculum on Todd-Hewitt/5% blood agar plates. All mice were killed 3 or 4 days after infection. During the infection process, challenged mice were monitored for the development of symptoms associated with the onset of S. agalactiae induced-disease. Typical symptoms in an appropriate order included piloerection, an increasingly hunched posture, discharge from eyes, increased lethargy and reluctance to move which was often the result of apparent paralysis in the lower body/hind leg region. The latter symptoms usually coincided with the development of a moribund state at which stage the mice were culled to prevent further suffering. These mice were deemed to be very close to death, and the time of culling was used to determine a survival time for statistical analysis. Where mice were found dead, a survival time was calculated by averaging the time when a particular mouse was last observed alive and the time when found dead, in order to determine a more accurate time of death.

Interpretation of Results

A positive result was taken as any DNA sequence that was cloned and used in challenge experiments as described above and gave protection against that challenge. DNA sequences were determined to be protective;

-   -   if that DNA sequence gave statistically significant protection         (to a 95% confidence level (p>0.05) as determined using the         Mann-Whitney U test.     -   if that DNA sequence was marginal or non-significant using         Mann-Whitney but showed some protective features. For example,         one or more outlying mice may survive for significantly longer         time periods when compared with control mice. Alternatively, the         time to first death may also be prolonged when compared to         counterpart mice in control groups.

It is acceptable to allow marginal or non-significant results to be considered as potential positives when it is possible that the clarity of some results may be affected by problems associated with the administration of the DNA vaccine. Indeed, much varied survival times may reflect different levels of immune response between different members of a given group.

Results

Statistical Analysis of Survival Times—LEEP DNA Immunisation and GBS Challenge Trial 1 (FIG. 4 a) Mean Survival Times (hours) pcDNA3.1 17(ID-8) 18(ID-9) 20(ID-25) rib 1 26.833 14.916 27.750 30.500 88.666 2 42.333 94.000 34.333 33.333 28.166 (T) 3 47.916 45.166 41.083 34.083 37.250 4 28.333 30.750 47.083 23.500 37.250 5 42.333 74.666 94.000 94.000 94.000 (T) (T) (T) 6 25.333 25.000 26.166 30.500 45.750 Mean 37.549 51.899 48.849 43.083 57.066 sd 9.3943 32.214 26.257 28.768 31.556 p value 1 0.4049 0.4049 0.5000 0.1481 p value 2 >39.0123 >39.0 >39.0 >39.0 (T) - terminated at conclusion of experiment but showing symptoms of infection. p value 1 refers to statistical significance when compared to pcDNA3.1 controls. p value 2 refers to statistical significance when compared to rib positive control.

All DNA vaccine's showed a pattern of protection similar to that obtained with the rib DNA vaccine, which was initially used as a positive control.

17 (ID-8)

Mice immunised with the ‘17 (ID-8)’ DNA vaccine did not show significantly longer survival times when compared with the unvaccinated control group. However, there are two outlying mice one of which survived the term of the experiment despite developing symptoms. The group also exhibited a much wider range of survival times reflected by a mean survival value which is approximately 14 hours higher than that demonstrated by the unvaccinated control group.

18 (ID-9)

Mice immunised with the ‘18 (ID-9)’ DNA vaccine did not show significantly longer survival times when compared with the unvaccinated control group. However, there is one outlying mouse which survived the term of the experiment despite developing symptoms.

20 (ID-25)

Mice immunised with the ‘20 (ID-25)’ DNA vaccine did not show significantly longer survival times when compared with the unvaccinated control group. However, there was one outlying mouse which survived the term of the experiment despite developing symptoms.

Statistical Analysis of Survival Times—LEEP DNA Immunisation and GBS Challenge TRIAL 2 (FIG. 4 b) Mean Survival Times (hours) pcDNA UnVacc 22(ID-10) 28(ID-13) 1 45.000 27.916 44.666 72.000 (T) 2 37.333 45.083 51.416 33.000 3 37.333 37.583 40.791 36.083 4 35.291 24.583 44.666 72.000 (T) 5 24.333 37.583 36.916 49.166 6 45.000 33.166 57.833 36.083 Mean 35.858 34.549 43.691 52.449 sd 7.4342 8.2567 5.3825 18.850 p value 1 >39.0 0.1137 0.2340 p value 2 0.4679 0.0323 0.1137 (T) - terminated at conclusion of experiment but showing symptoms of infection. p value 1 refers to statistical significance when compared to pcDNA3.1 controls. p value 2 refers to statistical significance when compared to unvaccinated controls.

There was no significant difference in the survival times exhibited by the pcDNA3.1 and unvaccinated control groups. This is confirmed by their very similar mean survival times of 35.858 hours (pcDNA3.1) and 34.166 hours (Unvaccinated).

22 (ID-10)

Mice immunised with the ‘22 (ID-10)’ DNA vaccine exhibited significantly longer survival times when compared with the unvaccinated control group but not when compared with the pcDNA3.1 control group. In addition, the time to first death in this group was prolonged by approximately 12 hours when compared to the pcDNA3.1 and unvaccinated control groups. The mean survival time of 43.691 hours is also considerbly higher than that determined for both control groups.

28 (ID-13)

Mice immunised with the ‘28 (ID-13)’ DNA vaccine did not show significantly longer survival times when compared with the pcDNA3.1 and unvaccinated control groups. However there are three outlying mice, two of which survived the term of the experiment despite showing symptoms. In addition, the time to first death in this group was prolonged by approximately 9 hours when compared to the pcDNA3.1 and unvaccinated control groups. The mean survival time of 52.449 hours is also considerbly higher than that determined for both control groups, as well demonstrating a wider range of survival times.

Statistical Analysis of Survival Times—LEEP DNA Immunisation and GBS Challenge Trial 3 (FIG. 4 c) Mean Survival Times (hours) UnVacc. 70(ID-42) 94(ID-48) 86(ID-47) 15(ID-37) 1 27.583 25.166 34.666 32.416 43.749 2 27.583 42.666 49.500 32.416 38.333 3 24.583 34.666 27.000 42.500 50.666 4 22.250 42.666 30.500 34.500 45.166 5 35.916 30.583 30.500 34.500 69.082 6 22.250 25.166 42.666 42.500 31.166 Mean 27.583 35.149 34.433 35.266 49.399 sd 5.1691 7.6444 8.8495 4.1758 11.846 p value 0.0628 0.0321 0.0153 0.0041 p value refers to statistical significance when compared to unvaccinated controls. 70 (ID-42)

Mice immunised with the ‘70 (ID-42)’ DNA vaccine, marginally did not show significantly longer survival times when compared with the unvaccinated control group. However, the first death in this group is prolonged (by approximately 3 hours) when compared with the unvaccinated group. In addition, the group has a mean survival time which is approximately 8 hours longer than the unvaccinated group.

94 (ID-48)

Mice immunised with the ‘94 (ID-48)’ DNA vaccine exhibited significantly longer survival times when compared with the unvaccinated control group.

86 (ID-47)

Mice immunised with the ‘86 (ID-47)’ DNA vaccine exhibited significantly longer survival times when compared with the unvaccinated control group.

51 (ID-37)

Mice immunised with the ‘51 (ID-37)’ DNA vaccine exhibited significantly longer survival times when compared with the unvaccinated control group.

Statistical Analysis of Survival Times—LEEP DNA Immunisation and GBS Challenge Trial 4 (FIG. 4 d) Mean Survival Times (hours) UnVacc 9(ID-6) 1 32.666 35.250 2 21.666 30.958 3 23.916 69.333 4 22.999 52.333 5 25.916 44.916 6 35.916 47.083 Mean 25.432 46.041 sd 4.3291 16.096 p value 0.0101 (T) - terminated at conclusion of experiment but showing symptoms of infection. p value refers to statistical significance when compared to unvaccinated controls 9 (ID-6)

Mice immunised with the ‘39(ID-6)’ DNA vaccine showed significantly longer survival times when compared with the control group.

Statistical Analysis of Survival Times—LEEP DNA Immunisation and GBS Challenge Trial 6 (FIG. 4 e) Mean Survival Times (hours) pcDNA UnVacc 32(ID-15) 39(ID-17) 57(40) 1 33.541 36.000 25.041 52.333 28.333 2 36.750 29.999 30.458 44.750 32.708 3 36.750 32.749 44.833 44.750 36.083 4 36.750 44.500 30.458 36.250 40.333 5 29.000 28.333 64.833 36.250 72.000 (T) 6 30.750 31.666 72.000 28.583 33.750 (T) Mean 34.558 34.316 39.124 44.016 38.103 sd 3.4036 6.3921 16.140 13.833 12.986 p value 1 >39.0 0.4043 0.1867 0.4044 p value 2 0.2862 0.2873 0.0458 0.2113 (T) - terminated at conclusion of experiment but showing symptoms of infection. p value 1 refers to statistical significance when compared to pcDNA3.1 controls p value 2 refers to statistical significance when compared to unvaccinated controls.

There was no significant difference in the survival times exhibited by the pcDNA3.1 and unvaccinated control groups. This is confirmed by their very similar mean survival times of 34.558 hours (pcDNA3.1) and 34.316 hours (Unvaccinated).

32 (ID-15)

Mice immunised with the ‘32 (ID-15)’ DNA vaccine did not show significantly longer survival times when compared with the pcDNA3.1 and unvaccinated control groups. However, the ‘32 (ID-15)’ group has two outlying mice one of which survived the term of the experiment despite showing symptoms. This group also exhibits a wide range of survival times.

39 (ID-17)

Mice immunised with the ‘39 (ID-17)’ DNA vaccine exhibited significantly longer survival times when compared with the unvaccinated control group but was not significant when compared with the pcDNA3.1 control group. The group has a considerbly higher mean survival time of 44.016 hours than that determined for either of the control groups.

57 (ID-40)

Mice immunised with the ‘32 (ID-15)’ DNA vaccine did not show significantly longer survival times when compared with the pcDNA3.1 and unvaccinated control groups. However, the ‘32 (ID-15)’ group has one outlying mouse which survived the term of the experiment despite showing symptoms.

Survival Data-Set B

Statistical Analysis of Survival Times—LEEP DNA Immunisation and GBS Challenge Trial 2 (FIG. 5 a) Mean Survival Times (hours) pcDNA UnVacc 13(ID-72) 1 45.000 27.916 69.166 2 37.333 45.083 36.333 3 37.333 37.583 43.916 4 35.291 24.583 32.166 5 24.333 37.583 36.333 6 45.000 33.166 43.916 Mean 35.858 34.549 43.582 sd 7.4342 8.2567 14.917 p value 1 >39.0 0.4679 p value 2 0.4679 0.1880 p value 1 refers to statistical significance when compared to pcDNA3.1 controls. p value 2 refers to statistical significance when compared to unvaccinated controls.

There was no significant difference in the survival times exhibited by the pcDNA3.1 and unvaccinated control groups. This is confirmed by their very similar mean survival times of 35.858 hours (pcDNA3.1) and 34.166 hours (Unvaccinated).

13 (ID-72)

Mice immunised with the ‘13 (ID-72)’ DNA vaccine did not show significantly longer survival times when compared with the pcDNA3.1 and unvaccinated control groups. However, there is one outlying mouse which survived approximately 24 hours longer than the longest surviving mice in the pcDNA3.1 and unvaccinated control groups respectively. In addition, the time to first death in this group was prolonged when compared to the pcDNA3.1 and unvaccinated control groups. The mean survival time of 43.582 hours is considerbly higher than that determined for both control groups.

Statistical Analysis of Survival Times—LEEP DNA Immunisation and GBS Challenge Trial 3 (FIG. 5 b) Mean Survival Times (hours) UnVacc 3-60(ID-65) 3-5(ID-66) 1 27.583 54.416 42.916 2 27.583 31.000 42.916 3 24.583 43.000 32.874 4 22.250 34.916 42.916 5 35.916 38.958 27.333 6 22.250 34.916 30.916 Mean 27.583 40.458 37.791 sd 5.1691 8.9959 7.2860 p value 0.0098 0.0215 p value refers to statistical significance when compared to unvaccinated controls. 3-60 (ID-65)

Mice immunised with the ‘3-60 (ID-65)’ DNA vaccine exhibited significantly longer survival times when compared with the unvaccinated control group.

3-5 (ID-66)

Mice immunised with the ‘3-5 (ID-66)’ DNA vaccine exhibited significantly longer survival times when compared with the unvaccinated control group.

Statistical Analysis of Survival Times—LEEP DNA Immunisation and GBS Challenge Trial 4 (FIG. 5 c) Mean Survival Times (hours) UnVacc 3-40(ID-67) 3-30(ID-68) 3-38(ID-69) 1 32.666 79.750 35.500 68.583 2 21.666 35.833 28.333 29.916 3 23.916 30.500 31.208 29.916 4 22.999 22.708 98.000 31.041 (T) 5 25.916 28.583 73.500 32.166 6 35.916 40.791 32.333 29.916 Mean 25.432 39.474 53.308 38.324 sd 4.3291 22.998 30.961 16.940 p value 0.1149 0.0463 0.1132 (T) - terminated at conclusion of experiment but showing symptoms of infection. p value refers to statistical significance when compared to unvaccinated controls 3-40 (ID-67)

Mice immunised with the ‘3-40 (ID-67)’ DNA vaccine did not show significantly longer survival times when compared with the unvaccinated control group. However, there is one outlying mouse which survived approximately 43 hours longer than the longest surviving mice in the unvaccinated control group.

3-30 (ID-68)

Mice immunised with the ‘3-30 (ID-68)’ DNA vaccine exhibited significantly longer survival times when compared with the unvaccinated control group.

3-38 (ID-69)

Mice immunised with the ‘2-19 (ID-73)’ DNA vaccine did not show significantly longer survival times when compared with the unvaccinated control group. However, there was one outlying mouse which survived approximately 32 hours longer than the longest surviving mice in the unvaccinated control group. In addition, the time to first death was prolonged (by approximately 8 hours) when compared to the unvaccinated controls.

Statistical Analysis of Survival Times—LEEP DNA Immunisation and GBS Challenge Trial 5 (FIG. 5 d) Mean Survival Times (hours) UnVacc 141(ID-70) 3-20(ID-71) 2-19(ID-73) 3-6(ID-74) 1 27.833 47.500 36.166 36.166 44.666 2 45.666 52.833 44.833 49.833 36.000 3 45.666 49.333 26.750 55.833 75.416 4 34.333 46.250 36.166 68.583 36.000 5 34.333 47.500 55.916 33.333 55.916 6 45.666 36.500 44.833 30.583 36.000 Mean 37.566 48.683 37.234 48.749 49.599 sd 7.8558 2.5672 8.4103 14.497 16.587 p value 0.0101 0.5000 0.2336 0.1854 p value - refers to statistical significance when compared to unvaccinated controls. 141 (ID-70)

Mice immunised with the ‘141 (ID-70)’ DNA vaccine exhibited significantly longer survival times when compared with the unvaccinated control group.

3-20 (ID-71)

Mice immunised with the ‘3-20 (ID-71)’ DNA vaccine did not show significantly longer survival times when compared with the unvaccinated control group. However, there is one outlying mouse which survived approximately 10 hours longer than the longest surviving mice in the unvaccinated control group.

2-19 (ID-73)

Mice immunised with the ‘2-19 (ID-73)’ DNA vaccine did not show significantly longer survival times when compared with the unvaccinated control group. However, there are three outlying mouse which survived approximately 4, 10 and 23 hours longer than the longest surviving mice in the unvaccinated control group. This is reflected in the higher mean survival time of 48.749 hours and a much wider range of survival times.

3-6 (ID-74)

Mice immunised with the ‘3-6 (ID-74)’ DNA vaccine did not show significantly longer survival times when compared with the unvaccinated control group. However, there are three outlying mouse which survived approximately 4, 10 and 23 hours longer than the longest surviving mice in the unvaccinated control group. This is reflected in the higher mean survival time of 49.599 hours and a much wider range of survival times.

Statistical Analysis of Survival Times—LEEP DNA Immunisation and GBS Challenge Trial 6 (FIG. 5 e) Mean Survival Times (hours) pcDNA3.1 UnVacc. 3-51(ID-75) 3-56(ID-76) 1 33.541 36.000 36.333 46.583 2 36.750 29.999 30.291 29.833 3 36.750 32.749 32.000 40.166 4 36.750 44.500 52.333 46.583 5 29.000 28.333 72.000 46.583 (T) 6 30.750 31.666 40.499 — Mean 34.558 34.316 44.591 40.791 sd 3.4036 6.3921 16.615 7.9070 p value 1 >39.0 0.1876 0.0386 p value 2 0.2862 0.0867 0.0587 (T) - terminated at conclusion of experiment but showing symptoms of infection. p value 1 refers to statistical significance when compared to pcDNA3.1 controls p value 2 refers to statistical significance when compared to unvaccinated controls.

There was no significant difference in the survival times exhibited by the pcDNA3.1 and unvaccinated control groups. This is confirmed by their very similar mean survival times of 34.558 hours (pcDNA3.1) and 34.316 hours (Unvaccinated).

3-51 (ID-75)

Mice immunised with the ‘3-51 (ID-75)’ DNA vaccine did not show significantly longer survival times when compared with the pcDNA3.1 control group but was relatively close to significant when compared with the unvaccinated control group. The ‘3-51’ group has two outlying mouse one of which survived the term of the experiment despite developing symptoms. The mean survival time of 44.499 hours is considerbly higher than that determined for both control groups and the group also demonstrates as a much wider range of survival times.

3-56 (ID-76)

Mice immunised with the ‘3-56 (ID-76)’ DNA vaccine exhibited significantly longer survival times when compared with the pcDNA3.1 control group but were marginally not significant when compared with unvaccinated control group.

EXAMPLE 3 Conservation and Varability of Candidate Vaccine Antigen Genes Among Different Isolates of Group B Strepococci

An initial Southern blot analysis was carried out to determine cross-serotype conservation of novel Group B Streptococcal genes isolated using the LEEP system. Analysing the serotype distribution of a target gene will also determine their potential use as antigen components in a GBS vaccine. The Group B Streptococcal strains whose DNA was analysed as part of this study are listed in APPENDIX II.

Amplification and Labelling of Specific Target Genes as DNA Probes for Southern Blot Analysis.

Oligonucleotide primers were designed for each individual gene of interest derived using the LEEP system. Primers were designed to target the whole of the gene being investigated (All primers are listed in APPENDIX III). Specific gene targets were amplified by PCR using Vent DNA polymerase (NEB) according to the manufacturers instructions. Typical reactions were carried out in a 100 μl volume containing 50 ng of GBS template DNA, a one tenth volume of enzyme reaction buffer, 1 μM of each primer, 250 μM of each dNTP and 2 units of Vent DNA polymerase. A typical reaction contained an initial 2 minute denaturation at 95° C., followed by 35 cycles of denaturation at 95° C. for 30 seconds, annealing at the appropriate melting temperature for 30 seconds, and extension at 72° C. for 1 minute (1 minute per kilobase of DNA being amplified). The annealing temperature was determined by the lower melting temperature of the two oligonucleotide primers. The reaction was concluded with a final extension period of 10 minutes at 72° C.

All PCR amplified products were extracted once with phenol chloroform (2:1:1) and once with chloroform (1:1) and ethanol precipitated. Specific DNA fragments were isolated from agarose gels using the QIAquick Gel Extraction Kit (Qiagen). For use as DNA probes, purified amplified gene DNA fragments were labelled with digoxygenin using the DIG Nucleic Acid Labelling Kit (Boehringer Mannheim) according to the manufacturer's instructions.

Southern Blot Hybridisation Analysis of Group B Streptococcal Genomic DNA

Genomic DNA had previously been isolated from all strains of Group B Streptococci which were investigated for conservation of LEEP-derived gene targets. Appropriate DNA concentrations were digested using either Hin DIII, Eco RI or Bgl IIrestriction enzymes (NEB) according to manufacturer instructions and analysed by agarose gel electrophoresis. Following agarose gel electrophoresis of DNA samples, the gel was denatured in 0.25M HCl for 20 minutes and DNA was transferred onto Hybond™ N⁺ membrane (Amersham) by overnight capillary blotting. The method is essentially as described in Sambrook et al. (1989) using Whatman 3MM wicks on a platform over a reservoir of 0.4M NaOH. After transfer, the filter was washed briefly in 2×SSC and stored at 4 C in Saran wrap (Dow chemical company).

Filters were prehybridised, hybridised with the digoxygenin labelled DNA probes and washed using conditions recommended by Boehringer Mannheim when using their DIG Nucleic Acid Detection Kit. Filters were prehybridised at 68° C. for one hour in hybridisation buffer (1% w/v supplied blocking reagent, 5×SSC, 0.1% v/v N-lauryl sarcosine, 0.02% v/v sodium dodecyl sulphate[SDS]). The digoxygenin labelled DNA probe was denatured at 99.9° C. for 10 minutes before being added to the hybridisation buffer. Hybridisation was allowed to proceed overnight in a rotating Hybaid tube in a Hybaid Mini-hybridisation oven. Unbound probe was removed by washing the filter twice with 2×SSC-0.1% SDS for 5 minutes at room temperature. For increased stringency filters were then washed twice with 0.1×SSC-0.1% SDS for 15 minutes at 68° C. The DIG Nucleic Acid Detection Kit (Boehringer Mannheim) was used to immunologically detect specifically bound digoxygenin labelled DNA probes.

Results of Southern Blot Analysis

All genomic digests and their corresponding Southern blots followed an identical lane order as described in Table I. TABLE I Lane 1 2 3 4 5 6 7 strains 1 kb 515 A909 SB35 H36B 18RS21 1954/42 molecular serotype Weight Ia Ia Ib Ib II II Marker Lane 8 9 10 11 12 13 14 strains 118/158 97/0057 BM110 BS30 M781 97/0099 3139 serotype II II III III III III IV Lane 15 16 17 18 19 20 strains 1169- GBS 6 7271 JM9 Group A Streptococcus NT Strepococcus pneumoniae serotype V VI VII VIII — 14

For comparative purposes, it was decided to analyse the serotype distribution of the GBS rib gene, which encodes the known protective immunogen Rib. Rib has previously been shown to be present in sero type III and some strains of serotype II but not in serotypes Ia or Ib (Stalhammar-Carlemalm et al., 1993). Confirmation of this pattern would not only give increased confidence in interpreting subsequent results, it would also determine if a rib gene homologue was present in the remaining GBS serotypes being investigated here. Primers designed for the amplification of rib and its subsequent cloning into pcDNA3.1 (Appendix I), were used to generate a rib gene probe for Southern blot analysis.

Southern Blot Analysis—Rib (FIG. 6)

1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20

Genomic DNA from each strain was digested completely with Hin DIII (NEB) and electrophoresed at 40 Volts for 6 hours in 0.8% agarose, transferred onto Hybond N⁺ (Amersham) membrane by Southern blot and hybridised with the digoxigenin-labelled rib gene probe. Specifically bound DNA probe was identified using the DIG Nucleic Acid Detection Kit (Boehringer Mannheim).

Comment

The Southern blot analysis described in FIG. 7 indicates that the rib gene is not conserved across all GBS serotypes. rib appears to be absent from all serotype Ia and Ib strains (lanes 2 to 5) and from strains 118/158 and 97/0057 of serotype II (lanes 8 and 9). However, rib would appear to present in strains 18RS21 and 1954/92 of serotype II (lanes 6 and 7) and in all strains of serotype III (lanes 10 to 13). This is in agreement with previously published data (Stalhammar-Carlemalm et al., 1993). rib would also appear to be present in strains representing serotypes VII and VII (lanes 17 and 18) but was absent from strains representing serotypes IV, V and V (lanes 14 to 16) as well as the control strains (lanes 19 and 20). The rib gene probe did hybridise with lower intensity to genomic DNA fragments from strains representing serotypes Ia, lb, IV, VI, VII and serotype II strains 118/158 and 97/0057. This may indicate the presence of a gene in these strains with a lower level of homology to rib. These hybridising DNA fragments may contain a homologue of the GBS bca gene encoding the Ca protein antigen which has been shown to be closely homologous to the Rib protein (Wastfelt et al., 1996). If this is the case, it would be in agreement with previous work which showed all strains of serotypes Ia, Ib, II and III to be positive for one the two proteins (Stalhammar-Carlemalm et al., 1993). However, the apparent variable distribution of the rib gene amongst different GBS serotypes, makes it a less than ideal candidate for use in a GBS vaccine that is cross-protective against all serotypes.

Southern Blot Analysis—4 (ID-1) (Photograph 7)

1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20

Genomic DNA from each strain was digested completely with Hin DIII (NEB) and electrophoresed at 40 Volts for 6 hours in 0.8% agarose, transferred onto Hybond N⁺ (Amersham) membrane by Southern blot and hybridised with the digoxigenin-labelled 4 (ID-1) gene probe. Specifically bound DNA probe was identified using the DIG Nucleic Acid Detection Kit (Boehringer Mannheim).

Comment

The Southern blot analysis described in FIG. 7 indicates that gene 4 (ID-1) is conserved across all GBS serotypes. The gene probe hybridised specifically to a Hin DIII-digested genomic DNA fragment of approximately 3.5 kb in DNA digests from all GBS representatives. but was absent from both the control strains (lanes 19 and 20).

Southern Blot Analysis—5 (ID-2) (FIG. 8)

1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20

Genomic DNA from each strain was digested completely with Eco RI (NEB) and electrophoresed at 40 Volts for 6 hours in 0.8% agarose, transferred onto Hybond N⁺ (Amersham) membrane by Southern blot and hybridised with the digoxigenin-labelled 5 (ID-2) gene probe. Specifically bound DNA probe was identified using the DIG Nucleic Acid Detection Kit (Boehringer Mannheim).

Comment

The Southern blot analysis described in FIG. 7 indicates that gene 4 (ID-1) is conserved across all GBS serotypes. The gene probe hybridised specifically to a Eco RI-digested genomic DNA fragment of approximately 6.2 kb in DNA digests from all GBS representatives. but was absent from both the control strains (lanes 19 and 20).

Southern Blot Analysis—15 (ID-7) (FIG. 9)

1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20

Genomic DNA from each strain was digested completely with Eco RI (NEB) and electrophoresed at 40 Volts for 6 hours in 0.8% agarose, transferred onto Hybond N⁺ (Amersham) membrane by Southern blot and hybridised with the digoxigenin-labelled 15 (ID-7) gene probe. Specifically bound DNA probe was identified using the DIG Nucleic Acid Detection Kit (Boehringer Mannheim).

Comment

The Southern blot analysis described in FIG. 7 indicates that gene 15 (ID-7) is conserved across all GBS serotypes. The gene probe hybridised specifically to a Eco RI-digested genomic DNA fragment of approximately 6.2 kb in DNA digests from all GBS representatives. but was absent from both the control strains (lanes 19 and 20). The gene probe hybridised specifically with Eco RI-digested DNA fragments ranging from approximately 3.5 kb to 5.2 kb in size.

Southern Blot Analysis—17 (ID-8) (FIG. 10)

FIG. 5

1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20

Genomic DNA from each strain was digested completely with Hin DIII (NEB) and electrophoresed at 40 Volts for 6 hours in 0.8% agarose, transferred onto Hybond N⁺ (Amersham) membrane by Southern blot and hybridised with the digoxigenin-labelled 17 (ID-8) gene probe. Specifically bound DNA probe was identified using the DIG Nucleic Acid Detection Kit (Boehringer Mannheim).

Comment

The Southern blot analysis described in FIG. 7 indicates that gene 17 (ID-8) is conserved across all GBS serotypes. The gene probe hybridised specifically to a Hin DIII-digested genomic DNA fragment of approximately 2.3 kb in DNA digests from all GBS representatives. but was absent from both the control strains (lanes 19 and 20).

Southern Blot Analysis—22 (ID-10) (FIG. 11)

FIG. 6

1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20

Genomic DNA from each strain was digested completely with Bgl II (NEB) and electrophoresed at 40 Volts for 6 hours in 0.8% agarose, transferred onto Hybond N⁺ (Amersham) membrane by Southern blot and hybridised with the digoxigenin-labelled 22 (ID-10) gene probe. Specifically bound DNA probe was identified using the DIG Nucleic Acid Detection Kit (Boehringer Mannheim).

Comment

The Southern blot analysis described in FIG. 7 indicates that gene 22 (ID-10) is conserved across all GBS serotypes. The gene probe hybridised specifically to a Bgl II-digested genomic DNA fragment of approximately 3.1 kb in DNA digests from all GBS representatives except serotype Ib strain H₃₆B, where the gene probe hybridised specifically to a a Bgl II-digested genomic DNA fragment. Gene 22 (ID-10) was absent from both the control strains (lanes 19 and 20).

CONCLUSION

The Southern blot analyses described here, represents a preliminary investigation into the conservation level of LEEP-derived genes amongst different GBS serotypes. Initial results indicate that the genes 4 (ID-1), 5 (ID-2), 15 (ID-7), 17(ID-8) and 22 (ID-10) are present in all GBS serotypes and thus represent potential candidate genes for use in a GBS vaccine. Similar analyses are being currently carried out for each of the genes contained in this patent. APPENDIX I ID-8 (17) Forward Primer 5′- cgggatccgccaccatgACCACTTCTCAAGCTGTTTTAGC -3′ Reverse Primer 5′- ttgcggccgcACCGATTATCAACAAAGTTCTG -3′ ID-9 (18) Forward Primer 5′- cggatccgccaccatgGCTACTCATATTGGAAGTTACCAGC -3′ Reverse Primer 5′- ttgcggccgcAGGGTTTGTTGAAGTGTCTTG -3′ ID-10 (22) Forward Primer 5′- cggatccgccaccatgTATCTATATCATTTACCAATGCCC -3′ Reverse Primer 5′- ttgcggccgcTTTATGTATAGAAACAGCAGTCCC -3′ ID-13 (28) Forward Primer 5′- cggatccgccaccatgAAAGGAAGAACAACCTATTCGTTTAG -3′ Reverse Primer 5′- ttgcggccgcAAGAGCAAATTTTCGTATCTCCTC -3′ ID-15 (32) Forward Primer 5′- cggatccgccaccATGATTGTTGGACACGGAATTG -3′ Reverse Primer 5′- ttgcggccgcTTTTTCTTCCTCCAAAATAACACTAGC -3′ ID-17 (39) Forward Primer 5′- cggatccgccaccatgGCGACTAAAGAGTTAGGTGTTAG -3′ Reverse Primer 5′- ttgcggccgcTATAGTTTTAGTTTCAACTTGTCTAGATG -3′ ID-25 (20) Forward Primer 5′- cgggatccaccatgTATACGAGTTTACAACCAAATCATG -3′ Reverse Primer 5′- ttgcggccgcGTCAGCTCGTACTGTTTTTTTAGC -3′ ID-37 (51) Forward Primer 5′- cggatccgccaccatgTGTCAAATGAATAGTGAACATAAAAG -3′ Reverse Primer 5′- ttgcggccgcCTCAAATAATTTACCTCCAATTCG -3′ ID-40 (51) Forward Primer 5′- cggatccgccaccatgGCTCCATTCGAATTTAAAGATTC -3′ Reverse Primer 5′- ttgcggccgcTGATTTACCAGTTTGGAAGAGTTC -3′ ID-42 (70) Forward Primer 5′- cggatccgccaccATGAATACTATTTATAATACATTGAGAACAG - 3′ Reverse Primer 5′- ttgcggccgcTTCTTTGTTCCAACTTTCTGG -3′ ID-47 (86) Forward Primer 5′- cggatccgccaccATGATAGAGTGGATTCAAACACATTTAC -3′ Reverse Primer 5′- ttgcggccgcTTTATGACTCAAGCGACGTGTTA -3′ ID-48 94 Forward Primer 5′- cggatccgccaccATGGAGTTAGTAATTAGAGATATTCGTAAG Reverse Primer 5′- ttgcggccgcCTTGTCATATTCATCTCCCTTCAAC ID-67 (3-40) Forward Primer 5′- cggatccgccaccatgGCTAGTTTTGTCATGAATCATAATGAC - 3′ Reverse Primer 5′- ttgcggccgcGTTATTTGCTCGTTGTTTAGCTAAATC -3′ ID-68 (3-30) Forward Primer 5′- cggatccgccaccatgGCTCTTAGTTTTTTTATGGTTTCAGTTCAAGC - 3′ Reverse Primer 5′- ttgcggccgcGAAGGCACGGCCACCTCC -3′ ID-69 (3-38) Forward Primer 5′- cggatccgccaccatgGGTGAAACCCAAGATACCAATCAAGC -3′ Reverse Primer 5′- ttgcggccgcAACACCTGGTGGGGGTTTGG -3′ ID-70 (141) Forward Primer 5′- cggatccgccaccATGGCTGGGAATCGTAATAACG -3′ Reverse Primer 5′- ttgcggccgcAGCCGTCTCTAAAACAGGCTTG -3′ ID-71 (3-20) Forward Primer 5′- cggatccgccaccatgCTTCCAACGCAGCCGCAAAAC -3′ Reverse Primer 5′- ttgcggccgcATTTAGTGTTATTTCTCCTGTTGCATAATCC -3′ ID-72 (13) Forward Primer 5′- cgggatccaccatgTACACGCATATTGTTGAAAAAAG -3′ Reverse Primer 5′- ttgcggccgcAAATAATTTCTTTTGGTTGTTTG -3′ ID-73 (2-19) Forward Primer 5′- cggatccgccaccatgAGTAATCAAGAAGTTTCAGCAAGC -3′ Reverse Primer 5′- ttgcggccgcCCATTGTGGAATATCAGCTGAAG -3′ ID-74 (3-6) Forward Primer 5′- cggatccgccatgGTGCAGGCAGTGGTACCGCT -3′ Reverse Primer 5′- ttgcggccgcGCGCATTGTAACAAATTCCTCAG -3′ ID-75 (3-51) Forward Primer 5′- cgggatccaccatgGCTGCCGAGAAGCATAAAG -3′ Reverse Primer 5′- ttgcggccgcATTATTTAGCTGCTTTTTTAATGG -3′ ID-76 (3-56) Forward Primer 5′- cgggatccaccatgTGTCAGGTTGTTTATGCAAGTTTTC -3′ Reverse Primer 5′- ttgcggccgcTTTACTAATTGATAAAGAGCAACTTCG -3′ rib (control) Forward primer 5′- ggggtaccggccaccATGGCTGAAGTAATTTCAGGAAGT -3′ Reverse primer 5′- cggaattccgTTAATCCTCTTTTTTTCTTAGAAACAGAT

APPENDIX II

Listed below are the details (serotype and strain designation) of Group B Streptococcus strains whose DNA was analysed for gene conservation SEROTYPE STRAIN Ia 515 Ia A909 Ib SB35 Ib H36B II 18RS21 II 1954/92  II 118/158 II  97/0057 III BM110 III BS30 III M781 III  97/0099 IV 3139 V 1169/NT VI GBS VI VII 7271 VIII JM9

A group A Streptococcal strain (serotype Ml, strain NCTC8198) and Streptococcus pneumoniae (serotype 14) were also included in the analysis for control purposes. APPENDIX III ID-1 (4) forward primer 5′- atggaaaaaaatacttggaaaaaattac -3′ reverse primer 5′- ctattttgttttagcgatgtctttatc -3′ ID-2 (5) forward primer 5′- atgtcaaaacaaaaagtaacggcaac -3′ reverse primer 5′- ttatttatggccaataccataagttaattg ID-6 (9) forward primer 5′- atgaaaaaagttttttttctcatggctatg -3′ reverse primer 5′- ttacttcaactgttgatagagcacttcc -3′ ID-7 (15) forward primer 5′-ttgttcaattttataggttttagaacttgg -3′ reverse primer 5′- ttaattttcattgcgtctcaaacc -3′ ID-8 (17) forward primer 5′- atgacaaaaaaacttattattgctatattag -3′ reverse primer 5′- ttaacgattatcaacaaagttctgtac -3′ ID-10 (22) forward primer 5′- atgatacgccagtttttaagagaa -3′ reverse primer 5′- ttatttatgtatagaaacagcagtccc -3′

REFERENCES

-   Anderson, R., Gao, X.-M., Papakonstantinopoulou, A., Roberts, M. and     Dougan, G. (1996) Immune response in mice following immunisation     with DNA encoding fragment C of tetanus toxin. Infection and     Immunity, 64, 3168-3173. -   Kurar, E. and Splitter, G. A. (1997) Nucleic acid vaccination of     Brucella abortus ribosomal L7/L12 gene elicits immune response.     Vaccine, 15, 1851-57. -   Larsson, C., Stalhammar-Carlemalm, M., and Lindahl, G. 1996.     Experimental vaccination against Group B Streptococcus, an     encapsulated bacterium, with highly purified preparations of cell     surface proteins Rib and Infect. Immun. 64: 3518-3523 -   Larsson, C., Stalhammar-Carlemalm, M., and Lindahl, G. 1999.     Protection against experimental infection with Group B Streptococcus     by immunization with a bivalent protein vaccine. Vaccine. 17:454-458 -   Stalhammar-Carlemalm, M., Stenberg, L., and Lindahl, G. 1993.     Protein Rib: a novel Group B Streptococcal protein that confers     protective immunity and is expressed by most strains causing     invasive infections: J. Exp. Med. 177: 1593-1603 -   Wastfelt, M., Stalhammar-Carlemalm, M., (1996) Identification of a     family of Streptococcal surface proteins with extremely repetitive     structure. J. Biol. Chem. 271: 18892-18897. -   Zhang, D., Yang, X., Berry, J. Shen, C., McClarty, G. and     Brunham, R. C. (1997) DNA vaccination with the major outer-membrane     protein genes induces acquired immunity to Chlamydia trachomatis     (mouse pneumonitis) infection. Infection and Immunity, 176, 1035-40. 

1-23. (canceled)
 24. An isolated Group B Streptococcus polypeptide comprising the amino acid sequence of SEQ ID NO: 125, fragments, derivatives, and variants thereof, wherein said fragments, derivatives, and variants are able to protect against Group B Streptococcus challenge.
 25. The polypeptide of claim 24, wherein said polypeptide, fragments, and variants thereof have at least about 50% sequence identity to the amino acid sequence of SEQ ID NO: 125, wherein said polypeptide, derivatives, and variants thereof are able to protect against Group B Streptococcus challenge.
 26. An isolated nucleic acid molecule comprising: (i) the nucleic acid sequence of SEQ ID NO: 124 or the full complement thereof, wherein said sequences are able to protect against Group B Streptococcus challenge; (ii) the RNA equivalent of the sequence of SEQ ID NO: 124 or the full complement thereof, wherein said sequences are able to protect against Group B Streptococcus challenge; (iii) a nucleic acid molecule which encodes for the amino acid sequence of SEQ ID NO: 125 or the full complement thereof, wherein said sequences are able to protect against Group B Streptococcus challenge; (iv) a nucleic acid molecule which encodes for fragments and variants of the amino acid sequence of SEQ ID NO: 125 or the full complement thereof, wherein said fragments and variants are able to protect against Group B Streptococcus challenge; or (v) a sequence which has at least about 50% sequence identity with any of the sequences of (i), (ii), (iii), or (iv), or the full complement thereof, wherein said sequences are able to protect against Group B Streptococcus challenge.
 27. An isolated vector comprising the nucleic acid of claim
 26. 28. An isolated vector according to claim 27, further comprising nucleic acid sequences selected from the group consisting of promoters, enhancers, signal sequences, leader sequences, translation start and stop signals, DNA stability controlling regions, and a fusion partner.
 29. An isolated host cell comprising the vector of claim
 27. 30. The isolated host cell of claim 29, wherein said host cell is prokayrotic or eukaryotic.
 31. A method of transforming a host cell with the isolated vector of claim
 27. 32. An isolated antibody, an AFFIBODY, or a binding fragment of an antibody which binds to the polypeptide of claim
 24. 33. The antibody or binding fragment thereof of claim 32, wherein said antibody or a binding fragment of an antibody is monoclonal.
 34. The antibody or binding fragment thereof of claim 32, wherein said antibody or a binding fragment of an antibody is polyclonal.
 35. The antibody binding fragment of claim 32, wherein said binding fragment of an antibody is selected from the group consisting of Fab, F(ab′)₂, Fv, and scFv fragments.
 36. An immunogenic composition comprising an agent which is able to protect a subject against Group B Streptococcus challenge.
 37. The immunogenic composition of claim 36, wherein said composition is a vaccine.
 38. The immunogenic composition of claim 36, wherein said agent is an isolated Group B Streptococcus polypeptide comprising the amino acid sequence of SEQ ID NO: 125, fragments, derivatives, and variants thereof, wherein said fragments, derivatives, and variants are able to protect against Group B Streptococcus challenge.
 39. The polypeptide of claim 38, wherein said polypeptide, fragments, and variants thereof have at least about 50% sequence identity to the amino acid sequence of SEQ ID NO: 125, wherein said polypeptide, derivatives, and variants thereof are able to protect against Group B Streptococcus challenge.
 40. The immunogenic composition of claim 36, wherein said agent is an isolated nucleic acid molecule comprising: (i) the nucleic acid sequence of SEQ ID NO: 124 or the full complement thereof, wherein said sequences are able to protect against Group B Streptococcus challenge; (ii) the RNA equivalent of the sequence of SEQ ID NO: 124 or the full complement thereof, wherein said sequences are able to protect against Group B Streptococcus challenge; (iii) a nucleic acid molecule which encodes for the amino acid sequence of SEQ ID NO: 125 or the full complement thereof, wherein said sequences are able to protect against Group B Streptococcus challenge; (iv) a nucleic acid molecule which encodes for fragments and variants of the amino acid sequence of SEQ ID NO: 125 or the full complement thereof, wherein said fragments and variants are able to protect against Group B Streptococcus challenge; or (v) a sequence which has at least about 50% sequence identity with any of the sequences of (i), (ii), (iii), or (iv), or the full complement thereof, wherein said sequences are able to protect against Group B Streptococcus challenge.
 41. A method treatment or prophylaxis of Group B Streptococcus infection comprising administering the immunogenic composition of claim
 36. 42. A method of detecting Group B Streptococcus comprising contacting a sample to be tested with at least one polypeptide, fragment, or variant thereof of claim
 24. 43. A kit comprising at least one polypeptide, fragment, or variant thereof of claim
 24. 44. A method of detecting Group B Streptococcus comprising contacting a sample to be tested with at least one nucleic acid of claim
 26. 45. A kit comprising at least one nucleic acid of claim
 26. 46. A method of detecting Group B Streptococcus comprising contacting a sample to be tested with at least one antibody, AFFIBODY, or binding fragment of an antibody of claim
 32. 47. A kit comprising at least one antibody, AFFIBODY, or binding fragment of an antibody of claim
 32. 48. A method of screening for nucleic acid encoding bacterial cell envelope associated or surface antigens in gram positive bacteria comprising: (a) preparing a reporter vector comprising a nucleotide sequence encoding the mature form of the Staphylococcus nuclease gene and an upstream promoter region with DNA from a gram positive bacteria, (b) transforming the resultant vector into Lactococcus lactis cells, and (c) assaying for the secretion of Staphylococcus nuclease protein in the transformed cell.
 49. The method of claim 48, wherein the reporter vector is a pTREP1-nuc vector.
 50. The method of claim 48, wherein the gram positive bacteria is selected from the group consisting of Group B Streptococcus, Streptococcus pneumoniae, Staphylcoccus aureus, and pathogenic Group A Streptococci.
 51. A method of determining whether a polypeptide, fragment or variant thereof according to claim 24 is a potential antimicrobial target comprising: (a) step for inactivating said polypeptide to determine if it is essential for the survival of a Group B Streptococcus organism, (b) determining if said Group B Streptococcus organism with said inactivated polypeptide per step (a) is still viable, (c) if said Group B Streptococcus organism is still viable, then said polypeptide is not essential for said organism's survival, and thus is not a potential antimicrobial target, and (d) if said Group B Streptococcus organism is no longer viable, then said polypeptide is essential for said organism's survival, and thus is a potential antimicrobial target.
 52. An isolated pTREP1-nuc vector as shown in FIG.
 3. 